--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/scripts/parallel_launch.sh	Tue Jan 14 06:09:42 2020 -0500
@@ -0,0 +1,108 @@
+#!/bin/bash
+
+# PIDs are not re-used until PID_MAX_DEFAULT is reached.
+
+#requirement for the workflow
+#source /home/galaxy-bitlab/galaxy/tools/proteindocking/scripts/ADT_VENV/bin/activate
+
+
+# Reads a text file with commands to execute
+if [ $# -lt 1 ]; then
+	echo " ==== ERROR ... ====."
+	echo ""
+	echo "	usage:  $0 <execution file> [max cores]"
+	echo ""
+	echo "	MANDATORY	<execution file>: a text file containing one command per line"
+	echo "	OPTIONAL	[max cores]	: number of cores to use. Default is available cores minus one"
+	echo ""
+	exit -1
+fi
+
+input=$1
+cores=$(grep -c ^processor /proc/cpuinfo)
+cores=`expr $cores - 1`
+current_jobs=0
+pidArray=()
+jobsArray=()
+totalJobs=0
+executedJobs=0
+finishedJobs=0
+
+if [ $# -eq 2 ]; then
+	cores=$2
+fi
+
+echo "Using $cores cores"
+
+
+#initialize
+for ((i=0 ; i < $cores ; i++))
+do
+	pidArray[$i]=-1	
+done
+
+# read execution guide and launch jobs
+while IFS= read -r var
+do
+
+	jobsArray[$totalJobs]=$var
+	#echo "${jobsArray[$totalJobs]}"
+	totalJobs=`expr $totalJobs + 1`
+
+done < "$input"
+
+
+# control them and only launch as many as specified
+while [[ $executedJobs -lt $totalJobs || $finishedJobs -lt $totalJobs  ]]; do
+
+	# Execute job
+
+	if [[ $current_jobs -lt $cores ]]; then
+
+		${jobsArray[$executedJobs]} &
+		pid=$!
+		for ((i=0 ; i < $cores ; i++))
+		do
+			
+
+		        if [[ ${pidArray[$i]} -eq -1 && $executedJobs -lt $totalJobs ]]; then
+				pidArray[$i]=$pid
+				current_jobs=`expr $current_jobs + 1`
+				echo "PID: $pid JOBS: $current_jobs LAUNCHING: ${jobsArray[$executedJobs]}"
+				executedJobs=`expr $executedJobs + 1`
+				break
+			fi
+		done
+
+
+	fi
+
+	for ((i=0 ; i < $cores ; i++))
+	do
+		pid=${pidArray[$i]}
+		if [[ $pid -ne -1 ]]; then
+
+			ps -p $pid > /dev/null
+			if [[ $? == 1 ]]; then
+				current_jobs=`expr $current_jobs - 1`
+				finishedJobs=`expr $finishedJobs + 1`
+				echo "PID: $pid finished! Completed: $finishedJobs from total: $totalJobs"
+				pidArray[$i]=-1
+			fi
+
+		fi
+	done
+
+	sleep .01
+
+done
+
+
+#deactivate
+
+
+#for job in `jobs -p`
+#do
+	#echo $job
+#	wait $job
+#done